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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.10

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2021-04-21, 12:42 based on data in: C:\Users\ChengXin\PycharmProjects\untitled\pmultiqc\test_data\UPS1\unique-peptides-star-align-stricter-pep-protein-FDR\proteomics_lfq


        ProteomicsLFQ

        proteomicslfq is an example module to show how the MultQC pluginm system works.

        Experimental Design

        This plot shows the Proteomics Experimental Design

        This plot shows the Proteomics Experimental Design. You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html

        Showing 27/27 rows and 6/6 columns.
        Spectra FileFraction_GroupFractionLabelSampleMSstats_ConditionMSstats_BioReplicate
        UPS1_12500amol_R1.mzML
        1
        1
        1
        1
        UPS1|12500 amol
        1
        UPS1_12500amol_R2.mzML
        2
        1
        1
        1
        UPS1|12500 amol
        1
        UPS1_12500amol_R3.mzML
        3
        1
        1
        1
        UPS1|12500 amol
        1
        UPS1_125amol_R1.mzML
        4
        1
        1
        2
        UPS1|125 amol
        2
        UPS1_125amol_R2.mzML
        5
        1
        1
        2
        UPS1|125 amol
        2
        UPS1_125amol_R3.mzML
        6
        1
        1
        2
        UPS1|125 amol
        2
        UPS1_25000amol_R1.mzML
        7
        1
        1
        3
        UPS1|25000 amol
        3
        UPS1_25000amol_R2.mzML
        8
        1
        1
        3
        UPS1|25000 amol
        3
        UPS1_25000amol_R3.mzML
        9
        1
        1
        3
        UPS1|25000 amol
        3
        UPS1_2500amol_R1.mzML
        10
        1
        1
        4
        UPS1|2500 amol
        4
        UPS1_2500amol_R2.mzML
        11
        1
        1
        4
        UPS1|2500 amol
        4
        UPS1_2500amol_R3.mzML
        12
        1
        1
        4
        UPS1|2500 amol
        4
        UPS1_250amol_R1.mzML
        13
        1
        1
        5
        UPS1|250 amol
        5
        UPS1_250amol_R2.mzML
        14
        1
        1
        5
        UPS1|250 amol
        5
        UPS1_250amol_R3.mzML
        15
        1
        1
        5
        UPS1|250 amol
        5
        UPS1_50000amol_R1.mzML
        16
        1
        1
        6
        UPS1|50000 amol
        6
        UPS1_50000amol_R2.mzML
        17
        1
        1
        6
        UPS1|50000 amol
        6
        UPS1_50000amol_R3.mzML
        18
        1
        1
        6
        UPS1|50000 amol
        6
        UPS1_5000amol_R1.mzML
        19
        1
        1
        7
        UPS1|5000 amol
        7
        UPS1_5000amol_R2.mzML
        20
        1
        1
        7
        UPS1|5000 amol
        7
        UPS1_5000amol_R3.mzML
        21
        1
        1
        7
        UPS1|5000 amol
        7
        UPS1_500amol_R1.mzML
        22
        1
        1
        8
        UPS1|500 amol
        8
        UPS1_500amol_R2.mzML
        23
        1
        1
        8
        UPS1|500 amol
        8
        UPS1_500amol_R3.mzML
        24
        1
        1
        8
        UPS1|500 amol
        8
        UPS1_50amol_R1.mzML
        25
        1
        1
        9
        UPS1|50 amol
        9
        UPS1_50amol_R2.mzML
        26
        1
        1
        9
        UPS1|50 amol
        9
        UPS1_50amol_R3.mzML
        27
        1
        1
        9
        UPS1|50 amol
        9

        Summary Table

        This plot shows the ProteomicsLFQ pipeline summary statistics

        This plot shows the ProteomicsLFQ pipeline summary statistics

        Showing 1/1 rows and 4/4 columns.
        Total MS/MS SpectralTotal MS/MS Spectral IdentifiedIdentified MS/MS Spectral CoverageTotal Peptide CountTotal Protein Identified
        1035348
        402297
        38.86%
        8641
        1141

        Pipeline Result Statistics

        This plot shows the ProteomicsLFQ pipeline final result

        This plot shows the ProteomicsLFQ pipeline final result. Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、 and identified the number of modified peptide in the pipeline, eg.

        Showing 27/27 rows and 6/6 columns.
        Spectra FileSample Nameconditionfractionpeptide_nummodified_peptide_numprotein_num
        UPS1_12500amol_R1.mzML
        1
        UPS1|12500 amol
        1
        5994
        884
        1060
        UPS1_12500amol_R2.mzML
        1
        UPS1|12500 amol
        1
        6028
        875
        1043
        UPS1_12500amol_R3.mzML
        1
        UPS1|12500 amol
        1
        6048
        868
        1042
        UPS1_125amol_R1.mzML
        2
        UPS1|125 amol
        1
        6046
        812
        1024
        UPS1_125amol_R2.mzML
        2
        UPS1|125 amol
        1
        6087
        821
        1048
        UPS1_125amol_R3.mzML
        2
        UPS1|125 amol
        1
        6016
        826
        1046
        UPS1_25000amol_R1.mzML
        3
        UPS1|25000 amol
        1
        6041
        893
        1038
        UPS1_25000amol_R2.mzML
        3
        UPS1|25000 amol
        1
        5683
        831
        1018
        UPS1_25000amol_R3.mzML
        3
        UPS1|25000 amol
        1
        5854
        845
        1029
        UPS1_2500amol_R1.mzML
        4
        UPS1|2500 amol
        1
        5662
        771
        1027
        UPS1_2500amol_R2.mzML
        4
        UPS1|2500 amol
        1
        5776
        795
        1036
        UPS1_2500amol_R3.mzML
        4
        UPS1|2500 amol
        1
        5720
        786
        1034
        UPS1_250amol_R1.mzML
        5
        UPS1|250 amol
        1
        5965
        809
        1039
        UPS1_250amol_R2.mzML
        5
        UPS1|250 amol
        1
        5990
        808
        1042
        UPS1_250amol_R3.mzML
        5
        UPS1|250 amol
        1
        5982
        806
        1050
        UPS1_50000amol_R1.mzML
        6
        UPS1|50000 amol
        1
        6011
        905
        1025
        UPS1_50000amol_R2.mzML
        6
        UPS1|50000 amol
        1
        6032
        905
        1024
        UPS1_50000amol_R3.mzML
        6
        UPS1|50000 amol
        1
        6048
        918
        1021
        UPS1_5000amol_R1.mzML
        7
        UPS1|5000 amol
        1
        5794
        811
        1039
        UPS1_5000amol_R2.mzML
        7
        UPS1|5000 amol
        1
        5844
        807
        1043
        UPS1_5000amol_R3.mzML
        7
        UPS1|5000 amol
        1
        5795
        785
        1029
        UPS1_500amol_R1.mzML
        8
        UPS1|500 amol
        1
        5820
        810
        1025
        UPS1_500amol_R2.mzML
        8
        UPS1|500 amol
        1
        5770
        777
        1038
        UPS1_500amol_R3.mzML
        8
        UPS1|500 amol
        1
        5742
        800
        1033
        UPS1_50amol_R1.mzML
        9
        UPS1|50 amol
        1
        6297
        867
        1043
        UPS1_50amol_R2.mzML
        9
        UPS1|50 amol
        1
        6209
        854
        1057
        UPS1_50amol_R3.mzML
        9
        UPS1|50 amol
        1
        6142
        842
        1036

        Number of Peptides Per Proteins

        This plot shows the number of peptides per proteins in ProteomicsLFQ pipeline final result

        This longer description explains what exactly the numbers mean and supports markdown formatting. This means that we can do this:

        • Something important
        • Something else important
        • Best of all - some code

        Doesn't matter if this is copied from documentation - makes it easier for people to find quickly.

        loading..

        Quantification Result

        This plot shows the quantification information of peptidesin ProteomicsLFQ pipeline final result

        This longer description explains what exactly the numbers mean and supports markdown formatting. This means that we can do this:

        • Something important
        • Something else important
        • Best of all - some code

        Doesn't matter if this is copied from documentation - makes it easier for people to find quickly.

        Showing 50/50 rows and 28/28 columns.
        IDsequencepeptide_abundance_study_variable[1]peptide_abundance_study_variable[2]peptide_abundance_study_variable[3]peptide_abundance_study_variable[4]peptide_abundance_study_variable[5]peptide_abundance_study_variable[6]peptide_abundance_study_variable[7]peptide_abundance_study_variable[8]peptide_abundance_study_variable[9]peptide_abundance_study_variable[10]peptide_abundance_study_variable[11]peptide_abundance_study_variable[12]peptide_abundance_study_variable[13]peptide_abundance_study_variable[14]peptide_abundance_study_variable[15]peptide_abundance_study_variable[16]peptide_abundance_study_variable[17]peptide_abundance_study_variable[18]peptide_abundance_study_variable[19]peptide_abundance_study_variable[20]peptide_abundance_study_variable[21]peptide_abundance_study_variable[22]peptide_abundance_study_variable[23]peptide_abundance_study_variable[24]peptide_abundance_study_variable[25]peptide_abundance_study_variable[26]peptide_abundance_study_variable[27]
        1
        YPDIFPVMK
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        1840157.500000
        nan
        nan
        nan
        nan
        nan
        nan
        462184.093750
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        2
        KPASASSSSHGTTHSSASSTGSK
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        565603.000000
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        3
        HEDVHR
        109476.726562
        nan
        nan
        868943.437500
        973273.125000
        1443811.625000
        nan
        328236.750000
        nan
        2025771.625000
        1504683.625000
        446417.531250
        566792.000000
        1607156.250000
        1357169.625000
        nan
        nan
        nan
        1635159.875000
        1422424.625000
        562681.375000
        1391783.750000
        1094301.000000
        1164157.250000
        nan
        nan
        nan
        4
        HHNEGTVSK
        464123.750000
        nan
        nan
        nan
        402090.062500
        485311.312500
        nan
        651087.812500
        237535.671875
        3186425.000000
        573661.125000
        372533.343750
        2228138.500000
        432238.968750
        1492275.750000
        nan
        nan
        nan
        476860.250000
        548713.750000
        1331076.500000
        1545434.625000
        1542898.500000
        380893.656250
        nan
        nan
        nan
        5
        YDSTHGR
        1101987.500000
        1116074.250000
        1093054.125000
        nan
        nan
        nan
        947414.437500
        1522625.375000
        1230558.125000
        nan
        nan
        nan
        nan
        nan
        nan
        1319410.125000
        1354251.625000
        1361846.000000
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        6
        VLHHEK
        nan
        nan
        nan
        nan
        580918.437500
        928945.062500
        nan
        nan
        nan
        6931859.500000
        985525.937500
        nan
        6547256.000000
        1151918.125000
        1047077.687500
        nan
        nan
        nan
        1170664.750000
        837530.812500
        nan
        1252125.625000
        1044594.000000
        nan
        nan
        nan
        nan
        7
        GMAGGQHHHR
        nan
        nan
        nan
        177070.359375
        139076.796875
        111180.023438
        nan
        nan
        nan
        nan
        nan
        nan
        112377.156250
        126382.992188
        nan
        710121.500000
        1383629.250000
        299415.343750
        nan
        nan
        nan
        118663.515625
        161408.109375
        100469.937500
        2693810.750000
        4095009.500000
        3789387.500000
        8
        GHDSADHASQNSGGKPR
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        345763.156250
        544731.000000
        nan
        nan
        1332536.125000
        nan
        nan
        nan
        1061641.125000
        538018.500000
        254869.406250
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        9
        HAHGDQYK
        2280078.250000
        3058346.000000
        4806464.000000
        3608151.250000
        717448.062500
        569066.687500
        4421043.000000
        1729560.750000
        1348484.250000
        417204.093750
        1329214.750000
        1609287.375000
        1570276.000000
        716054.062500
        1961560.625000
        691154.125000
        231055.265625
        nan
        1249660.250000
        1995489.250000
        2043329.375000
        1213144.375000
        879403.750000
        1199378.125000
        nan
        1507238.125000
        2771405.250000
        10
        HIDAGAKK
        1032032.437500
        nan
        nan
        4259017.500000
        5748595.500000
        8919048.000000
        nan
        3460807.250000
        4579716.000000
        6444793.000000
        2457546.250000
        1129948.000000
        20178290.000000
        11155031.000000
        7866368.500000
        nan
        nan
        nan
        2460415.250000
        1853720.500000
        1162547.875000
        10095528.000000
        8613210.000000
        7369748.000000
        nan
        nan
        nan
        11
        TVDGPSHK
        1107416.000000
        1094882.500000
        1106273.875000
        nan
        nan
        nan
        1047103.625000
        1834514.375000
        1503664.125000
        nan
        nan
        975960.187500
        nan
        nan
        nan
        1482506.000000
        1408446.875000
        1444747.250000
        nan
        973444.812500
        nan
        nan
        nan
        nan
        nan
        nan
        312946.656250
        12
        HLKSEDEMK
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        467333.562500
        nan
        nan
        nan
        nan
        nan
        nan
        146740.046875
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        13
        KRPVPK
        4096939.250000
        1771598.000000
        nan
        5403828.500000
        13136981.000000
        18317704.000000
        1588964.250000
        9759575.000000
        3039966.000000
        26625894.000000
        7801262.000000
        6247166.500000
        22657700.000000
        23035096.000000
        18708216.000000
        nan
        nan
        nan
        7269465.500000
        6782982.500000
        nan
        22446564.000000
        21772338.000000
        19004282.000000
        nan
        nan
        nan
        14
        KKDDVVK
        667884.000000
        nan
        nan
        1960188.625000
        2153081.250000
        nan
        nan
        1583934.625000
        587978.312500
        nan
        4491909.500000
        1094901.500000
        nan
        4265950.000000
        3428231.750000
        nan
        nan
        nan
        2214772.500000
        1921190.750000
        nan
        nan
        nan
        3358303.000000
        nan
        nan
        nan
        15
        VHGEEDPTKK
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        409504.812500
        nan
        nan
        711285.312500
        nan
        nan
        685727.500000
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        16
        DKSEAPKEEAGETNK
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        1187067.750000
        790827.687500
        572823.500000
        1017232.750000
        nan
        888972.875000
        nan
        nan
        nan
        852340.687500
        770119.000000
        552103.500000
        nan
        623865.750000
        nan
        nan
        nan
        nan
        17
        AQNEFDDLIAAQQNAINR
        nan
        453164.656250
        nan
        nan
        907825.812500
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        18
        KLSEESKR
        1283963.375000
        nan
        342705.750000
        1084562.500000
        1337588.625000
        1398166.375000
        376283.156250
        1318315.000000
        nan
        nan
        nan
        nan
        nan
        1815091.875000
        1701211.250000
        nan
        nan
        nan
        nan
        1362353.250000
        nan
        1666363.500000
        1864397.375000
        1773918.125000
        nan
        nan
        nan
        19
        KKAPAGGAADAAAK
        627051.437500
        488833.562500
        220769.015625
        1273792.500000
        1291778.375000
        1548640.750000
        405325.031250
        1684237.500000
        862098.062500
        1761354.625000
        1235612.250000
        979589.812500
        2235350.750000
        1610879.125000
        1233862.000000
        nan
        nan
        nan
        2201255.750000
        1279841.000000
        849178.000000
        1704349.750000
        1617460.500000
        1991755.625000
        nan
        nan
        291959.906250
        20
        KKAPAGGAADAAAK
        1599213.250000
        1170798.875000
        792742.625000
        2301550.750000
        2846155.000000
        3086109.000000
        1110898.250000
        3001132.750000
        1383964.500000
        4161654.500000
        2870802.750000
        2281553.500000
        3831100.000000
        3462922.500000
        2961193.750000
        nan
        nan
        nan
        3197624.500000
        3161641.000000
        2552778.750000
        4262905.500000
        3194209.500000
        3614427.250000
        nan
        nan
        nan
        21
        TNLANNKKPEK
        nan
        nan
        nan
        nan
        242056.562500
        nan
        nan
        nan
        nan
        256866.000000
        nan
        nan
        401173.437500
        250875.515625
        nan
        nan
        nan
        nan
        104897.625000
        nan
        nan
        nan
        225022.109375
        nan
        nan
        nan
        nan
        22
        YKGTVSHDDK
        nan
        nan
        nan
        745394.187500
        926810.062500
        1197871.250000
        nan
        227097.421875
        nan
        1904860.875000
        308576.687500
        989201.625000
        1933637.000000
        1436696.500000
        1084902.375000
        nan
        nan
        nan
        448553.906250
        300968.875000
        nan
        1177250.000000
        995906.312500
        1027686.812500
        nan
        nan
        nan
        23
        KDKEACVHK
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        924877.062500
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        24
        KSNHNSHSSK
        nan
        42420.906250
        nan
        nan
        125068.109375
        nan
        nan
        nan
        nan
        nan
        nan
        50755.507812
        nan
        nan
        29812.269531
        17920790.000000
        nan
        nan
        nan
        93155.328125
        nan
        nan
        nan
        35206.242188
        nan
        112332.296875
        165689.609375
        25
        RKPVTEAR
        7745268.500000
        6563301.000000
        3275418.750000
        nan
        nan
        nan
        14163414.000000
        16397588.000000
        23497936.000000
        nan
        nan
        nan
        nan
        nan
        nan
        6048500.000000
        1994620.875000
        711268.062500
        nan
        nan
        1003286.312500
        nan
        nan
        nan
        nan
        nan
        nan
        26
        DKAETLKK
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        1649725.750000
        nan
        nan
        nan
        nan
        nan
        27
        TVDKPVGSSHAQEK
        1087654.000000
        nan
        712078.062500
        nan
        nan
        nan
        809408.625000
        4356526.000000
        1229225.250000
        nan
        nan
        3127351.500000
        nan
        4112173.250000
        nan
        638375.562500
        nan
        nan
        nan
        nan
        1794375.750000
        nan
        nan
        nan
        nan
        nan
        nan
        28
        MYTSMGGIEPKELFVVGK
        1014291.375000
        nan
        nan
        nan
        nan
        1312638.875000
        nan
        nan
        nan
        nan
        nan
        1069588.125000
        nan
        1389739.875000
        1151548.375000
        nan
        nan
        nan
        1124897.875000
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        29
        HAEHIK
        14029094.000000
        3371087.250000
        2469402.250000
        8356236.000000
        9643225.000000
        13258996.000000
        2899025.500000
        15414948.000000
        4527445.000000
        12764215.000000
        3435167.500000
        10422591.000000
        15130254.000000
        15484127.000000
        8108705.000000
        411986.156250
        nan
        nan
        5342498.000000
        11226515.000000
        5128991.000000
        14184892.000000
        14711576.000000
        10341834.000000
        nan
        408263.031250
        3315672.750000
        30
        TAAHTHIK
        nan
        nan
        nan
        nan
        nan
        1112284.500000
        nan
        3858488.500000
        nan
        1999293.875000
        nan
        nan
        1897349.500000
        833695.687500
        nan
        nan
        nan
        nan
        1094428.000000
        951816.875000
        703354.187500
        nan
        nan
        nan
        nan
        nan
        nan
        31
        NQEKEQEEQQQQEGHNNKEEHK
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        980375.875000
        nan
        nan
        32
        YITTWENEFLDSQR
        nan
        nan
        nan
        2870124.500000
        3033221.000000
        2775493.250000
        nan
        nan
        nan
        3542714.500000
        3355702.250000
        nan
        nan
        3813569.250000
        nan
        3178990.250000
        2302877.500000
        nan
        3381872.250000
        nan
        nan
        4167244.250000
        2960200.000000
        3596930.750000
        1726941.750000
        nan
        2350442.250000
        33
        NQEKEQEEQQQQEGHNNKEEHK
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        1137302.500000
        nan
        nan
        34
        ESVELPLTHPELYEEMGIK
        11411398.000000
        10513610.000000
        10057162.000000
        12318296.000000
        12028681.000000
        12120105.000000
        nan
        11189504.000000
        8279938.500000
        nan
        11381284.000000
        10115129.000000
        nan
        nan
        11678262.000000
        nan
        nan
        nan
        11462310.000000
        10763830.000000
        nan
        12329036.000000
        nan
        10926950.000000
        10548748.000000
        10983786.000000
        nan
        35
        NRAPPQRPR
        2811862.750000
        2211249.250000
        1709423.250000
        4230651.500000
        4248479.000000
        nan
        1957498.500000
        5595389.000000
        3568202.250000
        nan
        nan
        2978061.000000
        4695404.000000
        4437060.000000
        4226828.500000
        nan
        982655.250000
        nan
        nan
        nan
        nan
        5193425.000000
        4885309.000000
        5091879.000000
        nan
        2663494.500000
        3328171.750000
        36
        TTHPVSHGHSGSSTGPK
        nan
        3910617.500000
        826134.125000
        nan
        nan
        nan
        1554253.250000
        3635082.500000
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        2751063.250000
        2206326.750000
        2093312.000000
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        37
        ISIFYNDPVSSLSFEPSEK
        nan
        2085545.375000
        nan
        2712102.500000
        2552041.750000
        2232902.750000
        2476055.000000
        nan
        nan
        2740629.500000
        2440785.000000
        2012215.750000
        2611126.250000
        2671558.250000
        2588230.000000
        nan
        nan
        nan
        nan
        nan
        nan
        2445257.750000
        nan
        2248239.250000
        nan
        2244465.500000
        2329184.000000
        38
        HGGYKPTDK
        6652318.000000
        nan
        4617961.500000
        nan
        nan
        nan
        8375124.000000
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        868357.312500
        3741051.750000
        nan
        nan
        nan
        nan
        nan
        nan
        39
        NRAPPQRPR
        15859674.000000
        12525075.000000
        11196810.000000
        20404692.000000
        21211894.000000
        22961512.000000
        13160327.000000
        22544720.000000
        17036694.000000
        20273794.000000
        17993640.000000
        13239553.000000
        25506238.000000
        23818112.000000
        22898912.000000
        6850638.500000
        4037292.750000
        2692088.750000
        18315890.000000
        17431416.000000
        17135450.000000
        25893876.000000
        25860502.000000
        25443398.000000
        4993516.000000
        12579233.000000
        15716877.000000
        40
        GPLLVQDVVFTDEMAHFDR
        nan
        nan
        nan
        2091046.250000
        nan
        nan
        nan
        nan
        1238773.500000
        nan
        nan
        nan
        nan
        nan
        1841220.000000
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        41
        VAFPHLYNSR
        3915472.250000
        3037630.500000
        nan
        3730903.000000
        3702929.250000
        3718040.000000
        2929945.250000
        7955066.500000
        3915474.500000
        nan
        5287930.000000
        4527166.500000
        5783935.000000
        6266120.000000
        4339188.500000
        nan
        nan
        nan
        5421850.500000
        4952504.500000
        4354241.500000
        4940784.000000
        nan
        4298189.000000
        nan
        nan
        nan
        42
        KLEDHPK
        123307104.000000
        106837896.000000
        84448032.000000
        78902920.000000
        89514744.000000
        98280312.000000
        87897472.000000
        208969872.000000
        151869680.000000
        153749568.000000
        135967648.000000
        134893232.000000
        120237632.000000
        119641896.000000
        116114464.000000
        29000224.000000
        9957461.000000
        4593758.500000
        144472032.000000
        139470512.000000
        134152640.000000
        118353248.000000
        119820968.000000
        124538512.000000
        1584150.125000
        31069960.000000
        52193336.000000
        43
        ISIFYNDPVSSLSFEPSEK
        5685108.500000
        nan
        nan
        nan
        nan
        nan
        nan
        9017005.000000
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        5305006.500000
        nan
        nan
        44
        NRAPPQRPR
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        15836175.000000
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        23359370.000000
        nan
        nan
        nan
        45
        GMAGGQHHHR
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        1213020.500000
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        5626264.000000
        46
        KVAHTSYK
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        2110450.500000
        1801976.625000
        47
        NDTFALIGYGSQGYGQGLNLR
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        5376821.000000
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        48
        HASSPVKR
        8809101.000000
        nan
        nan
        5355382.500000
        5685757.500000
        6055214.500000
        nan
        15897202.000000
        nan
        nan
        10585586.000000
        10470499.000000
        nan
        7152875.000000
        7125103.500000
        nan
        nan
        nan
        nan
        12019439.000000
        10120347.000000
        7329381.500000
        7291046.500000
        7503383.500000
        nan
        nan
        nan
        49
        KLDHTER
        10141804.000000
        nan
        nan
        nan
        nan
        nan
        11774413.000000
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        nan
        9861717.000000
        50
        KTEAANKVEETK
        25971638.000000
        22918974.000000
        19555502.000000
        14728844.000000
        16309011.000000
        17451486.000000
        19192068.000000
        53974216.000000
        40514532.000000
        30347864.000000
        26399548.000000
        25727130.000000
        20810596.000000
        20598182.000000
        21541504.000000
        28439596.000000
        23274622.000000
        21330412.000000
        25809874.000000
        24948762.000000
        24687260.000000
        19527478.000000
        18981324.000000
        20057154.000000
        6394581.500000
        9731348.000000
        12232300.000000
        First Page Previous PageNext Page Last PagePage/Total Pages

        Peptide-Spectrum Matches

        This plot shows the PSM informationin ProteomicsLFQ pipeline final result

        This longer description explains what exactly the numbers mean and supports markdown formatting. This means that we can do this:

        • Something important
        • Something else important
        • Best of all - some code

        Doesn't matter if this is copied from documentation - makes it easier for people to find quickly.

        Showing 50/50 rows and 3/3 columns.
        PSM_IDsequenceuniquesearch_engine_score[1]
        0
        YPDIFPVMK
        1
        0.020432400
        1
        YPDIFPVMK
        1
        0.049212900
        2
        KPASASSSSHGTTHSSASSTGSK
        1
        0.000000035
        3
        HEDVHR
        1
        0.000337860
        4
        HEDVHR
        1
        0.002171290
        5
        HEDVHR
        1
        0.000395317
        6
        HEDVHR
        1
        0.001292100
        7
        HEDVHR
        1
        0.001041510
        8
        HEDVHR
        1
        0.007875650
        9
        HEDVHR
        1
        0.000956745
        10
        HEDVHR
        1
        0.000783561
        11
        HEDVHR
        1
        0.001100610
        12
        HEDVHR
        1
        0.000617042
        13
        HEDVHR
        1
        0.001782390
        14
        HEDVHR
        1
        0.002193120
        15
        HEDVHR
        1
        0.002604750
        16
        HEDVHR
        1
        0.001791710
        17
        HEDVHR
        1
        0.002509710
        18
        HEDVHR
        1
        0.004418400
        19
        HEDVHR
        1
        0.000600523
        20
        HHNEGTVSK
        1
        0.000133779
        21
        HHNEGTVSK
        1
        0.000005448
        22
        HHNEGTVSK
        1
        0.000172128
        23
        HHNEGTVSK
        1
        0.000006248
        24
        HHNEGTVSK
        1
        0.000443889
        25
        HHNEGTVSK
        1
        0.000074277
        26
        HHNEGTVSK
        1
        0.000077329
        27
        HHNEGTVSK
        1
        0.000097670
        28
        HHNEGTVSK
        1
        0.000047111
        29
        HHNEGTVSK
        1
        0.000003528
        30
        HHNEGTVSK
        1
        0.000041733
        31
        HHNEGTVSK
        1
        0.000058530
        32
        HHNEGTVSK
        1
        0.000005865
        33
        HHNEGTVSK
        1
        0.030330400
        34
        HHNEGTVSK
        1
        0.000059593
        35
        HHNEGTVSK
        1
        0.000014703
        36
        HHNEGTVSK
        1
        0.000206862
        37
        YDSTHGR
        0
        0.000141769
        38
        YDSTHGR
        0
        0.000288653
        39
        YDSTHGR
        0
        0.000486917
        40
        YDSTHGR
        0
        0.000397113
        41
        YDSTHGR
        0
        0.000196494
        42
        YDSTHGR
        0
        0.000219259
        43
        YDSTHGR
        0
        0.000515477
        44
        YDSTHGR
        0
        0.000243188
        45
        YDSTHGR
        0
        0.000497314
        46
        VLHHEK
        1
        0.003729810
        47
        VLHHEK
        1
        0.004247390
        48
        VLHHEK
        1
        0.006562530
        49
        VLHHEK
        1
        0.004315360
        First Page Previous PageNext Page Last PagePage/Total Pages

        Spectra Tracking

        This plot shows the ProteomicsLFQ pipeline mzML tracking

        This longer description explains what exactly the numbers mean and supports markdown formatting. This means that we can do this:

        • Something important
        • Something else important
        • Best of all - some code

        Doesn't matter if this is copied from documentation - makes it easier for people to find quickly.

        Showing 27/27 rows and 6/6 columns.
        Spectra FileMS1_NumMS2_NumMSGFCometFinal result of spectraFinal result of Peptides
        UPS1_12500amol_R1.mzML
        7012
        39718
        26747
        26156
        15281
        4190
        UPS1_12500amol_R2.mzML
        6976
        39682
        26736
        26338
        15382
        4230
        UPS1_12500amol_R3.mzML
        6962
        39782
        26484
        26148
        15093
        4215
        UPS1_125amol_R1.mzML
        7277
        36802
        26205
        25778
        15086
        4389
        UPS1_125amol_R2.mzML
        7302
        36813
        25925
        25574
        14816
        4364
        UPS1_125amol_R3.mzML
        7306
        36871
        25809
        25470
        14424
        4204
        UPS1_25000amol_R1.mzML
        6836
        40856
        26907
        26481
        15840
        4298
        UPS1_25000amol_R2.mzML
        7018
        40512
        26684
        26116
        15244
        4045
        UPS1_25000amol_R3.mzML
        6973
        40439
        26849
        26242
        15712
        4194
        UPS1_2500amol_R1.mzML
        7269
        37482
        26117
        25603
        14596
        3936
        UPS1_2500amol_R2.mzML
        7247
        37556
        26193
        25775
        14663
        4025
        UPS1_2500amol_R3.mzML
        7211
        37739
        26067
        25376
        14169
        3992
        UPS1_250amol_R1.mzML
        7291
        36884
        26390
        25928
        15415
        4199
        UPS1_250amol_R2.mzML
        7275
        36887
        25977
        25394
        14587
        4139
        UPS1_250amol_R3.mzML
        7259
        37111
        26640
        26211
        15605
        4305
        UPS1_50000amol_R1.mzML
        6786
        41833
        26988
        26463
        15600
        4336
        UPS1_50000amol_R2.mzML
        6805
        41653
        26331
        26019
        14886
        4296
        UPS1_50000amol_R3.mzML
        6815
        41665
        26629
        26197
        15382
        4397
        UPS1_5000amol_R1.mzML
        7213
        37918
        26405
        25772
        14963
        4071
        UPS1_5000amol_R2.mzML
        7195
        38046
        26592
        26035
        15292
        4063
        UPS1_5000amol_R3.mzML
        7200
        38052
        26599
        25942
        13393
        3747
        UPS1_500amol_R1.mzML
        7314
        37009
        26350
        25905
        15228
        4093
        UPS1_500amol_R2.mzML
        7254
        37492
        26662
        26095
        15298
        4095
        UPS1_500amol_R3.mzML
        7288
        37342
        26426
        25873
        15003
        4070
        UPS1_50amol_R1.mzML
        7302
        36443
        25069
        24949
        13636
        4966
        UPS1_50amol_R2.mzML
        7336
        36416
        25251
        24910
        13619
        4590
        UPS1_50amol_R3.mzML
        7351
        36345
        25493
        25073
        14084
        4506

        Distribution of precursor charges

        This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.

        This information can be used to identify potential ionization problems including many 1+ charges from an ESI ionization source or an unexpected distribution of charges. MALDI experiments are expected to contain almost exclusively 1+ charged ions. An unexpected charge distribution may furthermore be caused by specific search engine parameter settings such as limiting the search to specific ion charges.

        loading..

        Number of Peaks per MS/MS spectrum

        This chart represents a histogram containing the number of peaks per MS/MS spectrum in a given experiment. This chart assumes centroid data. Too few peaks can identify poor fragmentation or a detector fault, as opposed to a large number of peaks representing very noisy spectra. This chart is extensively dependent on the pre-processing steps performed to the spectra (centroiding, deconvolution, peak picking approach, etc).

        loading..

        Peak Intensity Distribution

        This is a histogram representing the ion intensity vs. the frequency for all MS2 spectra in a whole given experiment. It is possible to filter the information for all, identified and unidentified spectra. This plot can give a general estimation of the noise level of the spectra.

        Generally, one should expect to have a high number of low intensity noise peaks with a low number of high intensity signal peaks. A disproportionate number of high signal peaks may indicate heavy spectrum pre-filtering or potential experimental problems. In the case of data reuse this plot can be useful in identifying the requirement for pre-processing of the spectra prior to any downstream analysis. The quality of the identifications is not linked to this data as most search engines perform internal spectrum pre-processing before matching the spectra. Thus, the spectra reported are not necessarily pre-processed since the search engine may have applied the pre-processing step internally. This pre-processing is not necessarily reported in the experimental metadata.

        loading..

        Delta Mass

        This chart represents the distribution of the relative frequency of experimental precursor ion mass (m/z) - theoretical precursor ion mass (m/z).

        Mass deltas close to zero reflect more accurate identifications and also that the reporting of the amino acid modifications and charges have been done accurately. This plot can highlight systematic bias if not centered on zero. Other distributions can reflect modifications not being reported properly. Also it is easy to see the different between the target and the decoys identifications.

        loading..